The journey to regulation of protein-based multiplex quantitative assays

Clinical Chemistry

Volumn 57, Issue 4, 2011, Pages 560-567

  Boja, Emily S ^a   Jortani, Saeed A ^b   Ritchie, James ^c   Hoofnagle, Andrew N ^d   Težak, Živana ^e   Mansfield, Elizabeth ^e   Keller, Penny ^f   Rivers, Robert C ^a   Rahbar, Amir ^a   Anderson, N Leigh ^g   Srinivas, Pothur ^h   Rodriguez, Henry ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b University of Louisville School of Medicine   (United States)

^c EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e CENTER FOR DEVICES AND RADIOLOGICAL HEALTH   (United States)

^f CENTERS FOR MEDICARE AND MEDICAID SERVICES   (United States)

^g The Plasma Proteome Institute   (United States)

^h NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PROTEIN;

ARTICLE; COHORT ANALYSIS; COMMUNITY; DIAGNOSTIC TEST; ENZYME LINKED IMMUNOSORBENT ASSAY; FOOD AND DRUG ADMINISTRATION; HUMAN; IMMUNOASSAY; IN VITRO STUDY; LABORATORY TEST; MASS SPECTROMETER; MASS SPECTROMETRY; MULTIPLEX PROTEIN BASED ASSAY; NATIONAL HEALTH ORGANIZATION; NEOPLASM; PHYSICIAN; PROGNOSIS; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ASSAY; REGULATORY MECHANISM; RISK ASSESSMENT; TREATMENT OUTCOME;

BIOLOGICAL MARKERS; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 79956155894     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2010.156034     Document Type: Article

References (21)

1. Polanski M, Anderson NL. A list of candidate cancer biomarkers for targeted proteomics. Biomark Insights 2007;1:1-48.
2. Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem 2010;56:177-85.
3. Hortin GL, Carr SA, Anderson NL. Introduction: advances in protein analysis for the clinical laboratory. Clin Chem 2009;56:149-51.
4. García-Foncillas J, Bandrés E, Zárate R, Remírez N. Proteomic analysis in cancer research: potential application in clinical use. Clin Transl Oncol 2006;8:250-61.
5. Wang P, Whiteaker JR, Paulovich AG. The evolving role of mass spectrometry in cancer biomarker discovery. Cancer Biol Ther 2009;8:1083-94.
6. Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P. The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin Appl 2008;2:1386-402.
7. Regnier FE, Skates SJ, Mesri M, Rodriguez H, Tezak Z, Kondratovich MV, et al. Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration. Clin Chem 2010; 56:165-71.
8. Whiteaker JR, Zhao L, Anderson L, Paulovich AG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol Cell Proteomics 2010;9:184-96.
9. Keshishian H, Addona T, Burgess M, Mani DR, Shi X, Kuhn E, et al. Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 2009;8:2339-49.
10. Anderson NL, Jackson A, Smith D, Hardie D, Borchers C, Pearson TW. SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. Mol Cell Proteomics 2009;8:995-1005.
11. Zhao M, Nolte D, Cho W, Regnier F, Varma M, Lawrence G, Pasqua J. High-speed interferometric detection of label-free immunoassays on the biological compact disc. Clin Chem 2006;52: 2135-40. (Pubitemid 44658228)
12. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010; 28:827-38.
13. Mansfield E, O'Leary TJ, Gutman SI. Food and Drug Administration regulation of in vitro diagnostic devices. J Mol Diagn 2005;7:2-7. (Pubitemid 40310159)
14. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, et al. Multi-site assessment of precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009;27:633-41.
15. Abramowski D, Wiederhold K, Furrer U, Jaton A, Neuenschwander A, Runser M, et al. Dynamics of Aβ turnover and deposition in different β-amyloid precursor protein transgenic mouse models following γ-secretase inhibition. J Pharmacol Exp Ther 2008;327:411-24.
16. Dodds MG, Frederiksen KS, Skak K, Hansen LT, Lundsgaard D, Thompson JA, Hughes SD. Immune activation in advanced cancer patients treated with recombinant IL-21: multianalyte profiling of serum proteins. Cancer Immunol Immunother 2009;58:843-54.
17. Wandall HH, Blixt O, Tarp MA, Pedersen JW, Bennett EP, Mandel U, et al. Cancer biomarkers defined by autoantibody signatures to aberrant O-glycopeptide epitopes. Cancer Res 2010;70: 1306-13.
18. Chen S, LaRoche T, Hamelinck D, Bergsma D, Brenner D, Simeone D, et al. Multiplexed analysis of glycan variation on native proteins captured by antibody microarrays. Nat Methods 2007;4: 437-44. (Pubitemid 46901278)
19. Ciccimaro E, Hanks SK, Yu KH, Blair IA. Absolute quantification of phosphorylation on the kinase activation loop of cellular focal adhesion kinase by stable isotope dilution liquid chromatography/mass spectrometry. Anal Chem 2009;81:3304-13.
20. Russek-Cohen E, Tezak Z, Philip R, Pastel M. Multivariate assays reporting a composite score. JSM Proceedings. CD ROM; 2007.
21. Rodriguez H, Tezak Z, Mesri M, Carr SA, Liebler DC, Fisher SJ, et al. Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA Interagency Oncology Task Force on Molecular Diagnostics. Clin Chem 2010; 56:237-43.